Although the field of genomics has recently sequenced thousands of genes from multiple species, it is much slower at providing information on assigning functions to these genes. Proteins are generally the effector molecules that ascribe roles to genes, and most of the functions of proteins arise through their three-dimensional structures and their interactions with other molecules. Conventional genetic and structural biology techniques have, respectively, been the most powerful avenues for determining the organization of cell signaling networks and the molecular details of protein structure and protein/protein interactions. Understanding protein structure and the protein:protein interactions of the cell at a basic level (i.e. identification of the molecules involved, determination of their molecular architecture, and elucidation of how these molecules interact with one another) is imperative for understanding how the disruption of a single element can result in human disease. X-ray crystallography and nuclear magnetic resonance spectroscopy are the current methods of choice for obtaining high resolution structural information. Mass spectrometry (MS) is an emerging technique that is showing tremendous potential for both identification of protein complexes and elucidation of protein structure, in particular for proteins that are not amenable to classical structural techniques. The advantages of MS sensitivity, low sample consumption, and the ability to analyze inhomogeneous mixtures can overcome the obstacles that hamper other structural methods. MS was actually developed about 100 years ago, but its utility in biological research is just now being realized. Using MS, we can probe the structure of a protein with chemical reagents and then assess inter-residue distances and solvent accessibility. These data can aid in the determination of the protein structure and, hence, as to how the protein works. Moreover, MS can also be employed to simultaneously determine what other proteins a particular protein of interest interacts with and how these interactions are formed. Protein:protein and protein:DNA interactions are often at the center of biological processes, both beneficial and harmful. The primary goal of this project is to determine structural features of protein interactions that are critical in biologically functional or in pathological processes. As examples, we are currently studying DNA repair enzyme interactions with DNA, the interaction surfaces in DNA mismatch repair enzymes, and structural transformations of proteins concomitant with phosphorylation that are involved in carcinogenesis.